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Adding first class Description field to SAMSequenceRecord #1209

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merged 1 commit into from
Nov 14, 2018

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lbergelson
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Checklist

  • Code compiles correctly
  • New tests covering changes and new functionality
  • All tests passing
  • Extended the README / documentation, if necessary
  • Is not backward compatible (breaks binary or source compatibility)

* The @sq DS header field was added to the 1.6 bam spec, this adds a getter and setter for it.
* We do not correctly support UTF-8 characters in description due to #1202
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codecov-io commented Oct 26, 2018

Codecov Report

Merging #1209 into master will increase coverage by 0.002%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #1209       +/-   ##
===============================================
+ Coverage     68.702%   68.704%   +0.002%     
- Complexity      8061      8063        +2     
===============================================
  Files            542       542               
  Lines          32711     32713        +2     
  Branches        5533      5533               
===============================================
+ Hits           22473     22475        +2     
  Misses          8038      8038               
  Partials        2200      2200
Impacted Files Coverage Δ Complexity Δ
...c/main/java/htsjdk/samtools/SAMSequenceRecord.java 71.429% <100%> (+0.697%) 36 <2> (+2) ⬆️

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@jamesemery jamesemery left a comment

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While I might contend that there are other first class attributes that don't have getters on SamSequenceRecord, those are independent of this being a useful change. 👍

@lbergelson lbergelson merged commit ce97a5f into master Nov 14, 2018
@lbergelson lbergelson deleted the lb_add_SQ_DS branch November 14, 2018 18:32
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3 participants